In a semiconductor manufacturing process, integrated circuits are fabricated within dies on a semiconductor wafer. The semiconductor wafer goes through many processing steps before the dies are separated by cutting the semiconductor wafer. The processing steps can include lithography, etching, doping, grinding, and/or depositing different materials. The processing steps can include wet and dry processing steps. Semiconductor wafers can be stacked or bonded on top of each other and separated along scribe lines to form what is referred to as a three-dimensional (“3D”) IC. The aforementioned processing steps can also be performed on bonded wafers. Contaminants, chemicals or residue from various processing steps that penetrate the die area of bonded wafers can limit production yield of dies formed therein.